Hi all,
I am mapping small RNA sequencing reads with bowtie1.2.2 to a locus that encodes a direct repeat with the exactly(!) the same sequence...
10 results in 0.0022 seconds.
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Bowtie1: Reads don't get randomly distributed on direct repeat
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Strange strand bias and unusual depths
Hi all,
I'm seeing some very strange stuff with a resequenced prokaryotic genome coming from an Illumina HiSeq 2000. The design is 50bp... -
Tandem repeats in gff/gtf format
Hi,
I am trying to find tandem repeats (mainly SINE,LINE, ERV) position in gff/gtf format. I don't know if such files exist but i will... -
perplexing bowtie2 repeat alignments
I am seeing something perplexing, can you help? I am trying to call variants in plasmids. To do this I am using bowtie2, freebayes and an assortment...Last edited by Mark; 07-12-2013, 07:40 AM. -
help in Repeat Masker
Can any of you please let me know the interpretation of the repeat families
This is the part of .out file generated by the RepeatMasker...Last edited by rahbz; 06-04-2013, 12:28 AM. -
young and old L1 subfamilies, Repeat Elements
I am interested to find which subfamilies of L1 elements belong to which "age" group. So far I have not found any such categorisation.
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Repeat masking
Hi everyone,
We have whole genome data from a number of tumour-normal pairs, and are looking at our score distributions for somatic changes.... -
How to bridge genome gaps resulting from repeats?
We sequenced a Pseudomonas genome which resulted in several 454 scaffolds. From examining the sequence data it looks like there are many gaps in the sequence... -
Segmentation fault in consed
I have assembled sequence data from half a 454 plate. The data was assembled with newbler and appears to have gaps due to problems resolving repeats e.g.... -
Newbler de novo assembly and repeats
Hi,
I'm using Newbler de novo assembler from the command line (runAssembly), with a set of 18,000 reads.
I'd like to tweak the "repeat"...
